Antechamber failure

[mayacheung@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22631
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
I am trying to prep a ligand for docking but when there is a failure running ANTECHAMBER for residue UNL. This has happened to be multiple times and I am not sure what to do. I have prepped a different ligand before and it worked fine so I am not sure why it is not working now.

Log:
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:/Users/mayac/OneDrive/Desktop/250 Project/compound9_ligand.mol"

> ui tool show "Dock Prep"

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Summary of feedback from adding hydrogens to compound9_ligand.mol #1  
---  
notes | Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
20 hydrogens added  
  
Closest equivalent command: addcharge standardizeResidues none  
Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue UNL (net charge +1) with am1-bcc method  
Running ANTECHAMBER command: C:/Program
Files/ChimeraX/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\mayac\AppData\Local\Temp\tmpj416qjnp\ante.in.mol2 -fi mol2 -o
C:\Users\mayac\AppData\Local\Temp\tmpj416qjnp\ante.out.mol2 -fo mol2 -c bcc
-nc 1 -j 5 -s 2 -dr n  
(UNL) ``  
(UNL) `Welcome to antechamber 20.0: molecular input file processor.`  
(UNL) ``  
(UNL) `Info: Finished reading file
(C:\Users\mayac\AppData\Local\Temp\tmpj416qjnp\ante.in.mol2); atoms read (44),
bonds read (46).`  
(UNL) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(UNL) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/bondtype" -j part
-i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(UNL) `bash.exe: warning: could not find /tmp, please create!`  
(UNL) ``  
(UNL) ``  
(UNL) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(UNL) `bash.exe: warning: could not find /tmp, please create!`  
(UNL) `Info: Total number of electrons: 182; net charge: 1`  
(UNL) ``  
(UNL) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/sqm" -O -i sqm.in
-o sqm.out`  
(UNL) `bash.exe: warning: could not find /tmp, please create!`  
  
Contents of sqm.out:

    
    
                --------------------------------------------------------
                                 AMBER SQM VERSION 19
     
                                         By
                  Ross C. Walker, Michael F. Crowley, Scott Brozell,
                             Tim Giese, Andreas W. Goetz,
                            Tai-Sung Lee and David A. Case
     
                --------------------------------------------------------
     
    
    --------------------------------------------------------------------------------
      QM CALCULATION INFO
    --------------------------------------------------------------------------------
    
    | QMMM: Citation for AMBER QMMM Run:
    | QMMM: R.C. Walker, M.F. Crowley and D.A. Case, J. COMP. CHEM. 29:1019, 2008
    
    QMMM: SINGLET STATE CALCULATION
    QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS = 63
    
    | QMMM: *** Selected Hamiltonian *** 
    | QMMM: AM1         
    
    | QMMM: *** Parameter sets in use ***
    | QMMM: C : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
    | QMMM: N : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
    | QMMM: F : M.J.S.DEWAR et al. THEOCHEM, 180, 1, (1988)
    | QMMM: O : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
    | QMMM: S : M.J.S.DEWAR et al. INORG. CHEM., 29, 3881, (1990)
    | QMMM: H : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
    
    | QMMM: *** SCF convergence criteria ***
    | QMMM: Energy change                :  0.1D-07 kcal/mol
    | QMMM: Error matrix |FP-PF|         :  0.1D+00 au
    | QMMM: Density matrix change        :  0.5D-05
    | QMMM: Maximum number of SCF cycles :     1000
    
    | QMMM: *** Diagonalization Routine Information ***
    | QMMM: Pseudo diagonalizations are allowed.
    | QMMM: Auto diagonalization routine selection is in use.
    | QMMM:
    | QMMM: Timing diagonalization routines:
    | QMMM:                              norbs =      116
    | QMMM:    diag iterations used for timing =       10
    | QMMM:
    | QMMM:              Internal diag routine = 0.065801 seconds
    | QMMM:                 Dspev diag routine = 0.035281 seconds
    | QMMM:                Dspevd diag routine = 0.024201 seconds
    | QMMM:                Dspevx diag routine = 0.128448 seconds
    | QMMM:                 Dsyev diag routine = 0.052337 seconds
    | QMMM:                Dsyevd diag routine = 0.039069 seconds
    | QMMM:                Dsyevr diag routine = 0.036476 seconds
    | QMMM:
    | QMMM:                Pseudo diag routine = 0.013025 seconds
    | QMMM:
    | QMMM: Using dspevd routine (diag_routine=3).
    
      QMMM: QM Region Cartesian Coordinates (*=link atom) 
      QMMM: QM_NO.   MM_NO.  ATOM         X         Y         Z
      QMMM:     1        1      C        2.6180    1.5330   -4.4630
      QMMM:     2        2      C        2.2650    2.8020   -4.9630
      QMMM:     3        3      C        1.1660    3.4920   -4.4190
      QMMM:     4        4      C        0.4070    2.9070   -3.3910
      QMMM:     5        5      C        0.7590    1.6400   -2.8860
      QMMM:     6        6      C        1.8790    0.9410   -3.4120
      QMMM:     7        7      C        2.2040   -0.3170   -2.8480
      QMMM:     8        8      N        0.0350    1.0980   -1.8740
      QMMM:     9        9      C        0.3590   -0.0810   -1.2770
      QMMM:    10       10      C        1.4480   -0.8290   -1.7750
      QMMM:    11       11      F        2.9580    3.3390   -5.9320
      QMMM:    12       12      O        3.1730   -0.9900   -3.2700
      QMMM:    13       13      C       -0.4030   -0.4810   -0.0700
      QMMM:    14       14      N        0.2250    0.0060    1.1830
      QMMM:    15       15      C        0.3370    1.4810    1.3040
      QMMM:    16       16      C        0.8420    1.9580    2.6960
      QMMM:    17       17      C       -0.0480    1.4720    3.8890
      QMMM:    18       18      C       -1.4460    1.9760    3.8540
      QMMM:    19       19      S       -3.9370    2.2710    3.3480
      QMMM:    20       20      C       -2.4910    1.2860    3.2210
      QMMM:    21       21      C       -1.8420    3.2040    4.4340
      QMMM:    22       22      C       -3.1830    3.5590    4.2660
      QMMM:    23       23      C        1.0330    3.5070    2.6780
      QMMM:    24       24      O        1.5250    3.9950    3.9230
      QMMM:    25       25      H        3.4610    1.0070   -4.8870
      QMMM:    26       26      H        0.9060    4.4720   -4.7920
      QMMM:    27       27      H       -0.4470    3.4300   -2.9870
      QMMM:    28       28      H       -0.7830    1.5930   -1.5480
      QMMM:    29       29      H        1.6980   -1.7840   -1.3380
      QMMM:    30       30      H       -1.4100   -0.0690   -0.1400
      QMMM:    31       31      H       -0.4670   -1.5690   -0.0360
      QMMM:    32       32      H       -0.3270   -0.3300    1.9590
      QMMM:    33       33      H        1.1500   -0.3920    1.2520
      QMMM:    34       34      H        1.0330    1.8370    0.5440
      QMMM:    35       35      H       -0.6420    1.9230    1.1160
      QMMM:    36       36      H        1.8300    1.5200    2.8410
      QMMM:    37       37      H        0.4130    1.8070    4.8180
      QMMM:    38       38      H       -0.0700    0.3820    3.8850
      QMMM:    39       39      H       -2.4180    0.3220    2.7410
      QMMM:    40       40      H       -1.1490    3.8300    4.9760
      QMMM:    41       41      H       -3.6630    4.4560    4.6310
      QMMM:    42       42      H        1.7440    3.7650    1.8920
      QMMM:    43       43      H        0.0760    3.9810    2.4620
      QMMM:    44       44      H        1.6300    4.9480    3.8740
    
    --------------------------------------------------------------------------------
      RESULTS
    --------------------------------------------------------------------------------
    
          iter         sqm energy              rms gradient
          ----    -------------------    -----------------------
    xmin    10       91.3357 kcal/mol        1.5593 kcal/(mol*A)
    xmin    20       90.7656 kcal/mol        0.2814 kcal/(mol*A)
    xmin    30       90.6410 kcal/mol        0.3855 kcal/(mol*A)
    xmin    40       90.4602 kcal/mol        0.8736 kcal/(mol*A)
    xmin    50       90.2729 kcal/mol        0.2639 kcal/(mol*A)
    xmin    60       90.1241 kcal/mol        0.2699 kcal/(mol*A)
    xmin    70       90.0355 kcal/mol        0.3978 kcal/(mol*A)
    xmin    80       89.9055 kcal/mol        0.3962 kcal/(mol*A)
    xmin    90       89.8435 kcal/mol        0.1990 kcal/(mol*A)
    xmin   100       89.7675 kcal/mol        0.3981 kcal/(mol*A)
    xmin   110       89.6974 kcal/mol        0.3630 kcal/(mol*A)
    xmin   120       89.6197 kcal/mol        0.3766 kcal/(mol*A)
    xmin   130       89.4753 kcal/mol        0.5124 kcal/(mol*A)
    

  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\add_charge\tool.py", line 263, in add_charges  
add_nonstandard_res_charges(self.session, residues, charge, method=method)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\add_charge\charge.py", line 330, in
add_nonstandard_res_charges  
nonstd_charge(session, tautomer_residues, net_charge, method, status=status)  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\add_charge\charge.py", line 634, in nonstd_charge  
raise ChargeError(ante_failure_msg)  
chimerax.add_charge.charge.ChargeError: Failure running ANTECHAMBER for
residue UNL  
Check reply log for details  
  
chimerax.add_charge.charge.ChargeError: Failure running ANTECHAMBER for
residue UNL  
Check reply log for details  
  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\add_charge\charge.py", line 634, in nonstd_charge  
raise ChargeError(ante_failure_msg)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 30.0.100.9805
OpenGL renderer: Intel(R) Iris(R) Plus Graphics
OpenGL vendor: Intel

Python: 3.11.2
Locale: en_CA.cp1252
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows

Manufacturer: Acer
Model: Spin SP314-54N
OS: Microsoft Windows 11 Home (Build 22631)
Memory: 8,367,693,824
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i5-1035G4 CPU @ 1.10GHz
OSLanguage: en-US

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    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.4
    urllib3: 2.1.0
    wcwidth: 0.2.13
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9
    WMI: 1.5.1
File attachment: compound9_ligand.mol

compound9_ligand.mol​

[mayacheung@…]

Added by email2trac

[Eric Pettersen]

Hi Maya,

Thanks for reporting this problem. I could not reproduce it. Computing charges for the structure you provided worked on my desktop Mac, as well as on a Windows 10 and Windows 11 box in my lab. So it's hard to say why it failed on your machine. Do you have access to any other machine to try this on?

--Eric

Eric Pettersen
UCSF Computer Graphics Lab